Ancient Protocol
by Spiras Stargate
Summary: They saw the problem the Asgard would have, long before they did and wanted to make sure they never had to deal with it themselves.
1. Chapter 1

Title: Ancient Protocol  
Rating: PG-13 - R (to be safe of course)  
Warnings: M/m &F/m pairings, fetishes, and a slight sex scene that will be later AND 'much girly high school drama' to quote one of my reviewers *smile*  
Disclaimer:I don't own this these characters, or the city, or even a puddle jumper! I'm not doing this for money either, just fun.

This is my first Atlantis fic so be gentle with your reviews as I'm not the best writer in the world. And please review...I like to know if I should even keep trying any more. Oh and I answer all of my reviews quickly or try to so don't be surprised if you hear from me. (If you don't want me to message you say so and I'll try to contain myself)

With that...I give you...this OOC piece of fan fiction.

* * *

"Zelenka to McKay."

Rodney jumped and his head slammed up against the bottom of the flight controls for the jumper he was working in.

"Ahh!" He hissed in pain and tapped the radio, "McKay."

"Something just popped up on the main screen in the control room."

McKay who had been rubbing the back of his head, paused, "It's not the deep space sensors again is it?"

"No…This is different. It looks like a count down of some kind."

"Right…Be right there. McKay out.

Elizabeth frowned, staring at the ticking numbers going by, "It says something about a Lantian Protocol…"

"What'd I miss?" Rodney came into the room from the stairs leading down into the control room from the jumper bay.

Radek pointed to the screen, "We were running a check on primary systems when this popped up. We can't get back into main system."

Rodney pulled over a laptop and started tapping away, "It looks like some sort of subroutine program."

Dr. Weir looked worried, "What is it?"

"Didn't I just say it looked like some sort of subroutine program? "Rodney gazed around at everyone else, who glared at him.

"Then there has to be some sort of code we can use to shut it down," Elizabeth folded her arms over her chest.

Rodney looked up from the laptop screen and pointed at the interface, "It says that this, whatever it is, initiates itself every few years while the city is occupied, so my guess would be that it has something to do with the people here or the computer systems."

"Rodney that isn't the point," she frowned at him, "we've lost control of primary systems and you don't seem worried about it!"

"Look…if it happens every few years than it shouldn't be a problem to just let it finish whatever its doing. The Ancient's aren't going to build something into their systems that could kill us all."

"So we're just supposed to wait? We don't even know what it's doing," Elizabeth was highly annoyed. "What if someone dials in? Or what if the Wraith show up and we need the cloak?"

Rodney went over and hit the shield button on the DHD and the clear glowing wall sprang into place. He hit it again and it shut off, "The DHD isn't affected. It seems that people could, if they wanted to, go off world while, whatever this is, was happening. As for the Wraith…the count down will have finished in less than 24 hours. If we need the cloak before then, I'd say we were done for any way."

"If people were able to leave the city during this, it _could_ be something dangerous," Elizabeth eyed Rodney, trying to get him to understand things from her view.

"That's highly unlikely. For all we know this could be a scheduled mandatory vacation. A program they made that forced the Lanteans into taking a break."

John chose then come up the stairs from the gate room floor, joining them in the control room, "What's going on?"

Elizabeth glanced at him, "We're not sure but Dr. McKay thinks there's no cause to be concerned."

The colonel looked up at the Ancient computer systems screen, "If everything's ok…then why has the auto destruct been turned on? And why is it in Ancient?"

Radek and Rodney looked at each other.

"It could be possible-" the Czech started.

"That doesn't make any sense!" Rodney snapped, looking at the screen worriedly for a moment before starting to type.

"What?" Elizabeth looked at Radek.

"It could be possible that Ancients feared their city would be over taken at some point, and they would not have time to destroy it," Radek pushed his glasses up his nose.

"But if it only happened every few years…then whoever took over Atlantis would just have to get whatever they wanted from the city and leave before it exploded," Elizabeth looked to Rodney, who was typing away again.

"Only if they were after stuff," John pointed out. "If they were after the city, eventually having it blow up on them would be better then them keeping it."

"Ha!" Rodney pointed down, "The data log of the Protocol says that each time this has happened, no one has aborted it. It was allowed to be carried through."

"And the city is still standing. Maybe Ancient Database is running its own check on systems."

Rodney pointed at Radek, "Of course! The system would have to lock everyone out of the primary systems while it checked for errors."

"And this stuff is pretty advanced so…it takes awhile," John leaned against one of the other consoles.

Elizabeth sighed, still looking at the screen, not entirely reassured, "Is there any other information about the program besides the data log Rodney?"

"Elizabeth it's-"

"Rodney, please. Humor me?"

The doctor sighed and started taping away on his laptop again.

John pushed off from the console, "Well if the city isn't in danger, I'm going to go find a turkey sandwich, because_ I_ haven't had lunch yet."

Radek watched the Colonel leave and then turned to look at Elizabeth for a moment, before moving his eyes to Rodney, "Have you finished with Jumper scenarios yet?"

"No! I got called away for this, but I'm almost finished with them," he turned the laptop around toward Elizabeth. "Good news is, even if we can't run the shield or anything like that, the information part of the Database is still accessible. There's _directly_ connected to the Protocol, but it's mentioned in other things."

"What does it say?" she picked up the laptop and started scrolling through the information.

"Well I don't know. I just found it," he gave her the look that said she was completely stupid. "But from what I can see, and my 'Ancient' is a little rusty, they used it as a passage of time," Rodney said almost amused.

"Then it must be something important," she stared at him, but he looked back at her unimpressed. "Why else would you use it for a passage of time? In ancient cultures on Earth, they would use significant events like eclipses or floods to show passages of time."

"Well the checking your highly advanced computer system for program errors _is _an important event," Rodney pointed back toward the stairs, "I have a jumper to finish scenarios on, so if you'll excuse me?" He left both Radek and Elizabeth, and hurried back up the stairs to the jumper bay.

She looked at Radek who had an apologetic look on his face, "He's not fun to be around when he is being –"

"Himself?" she smiled at him and put a hand on his shoulder, "Thanks."

The Czech blushed at the contact, but quickly recovered, "Yes well that and when he's about to-" the man stopped talking abruptly and looked her in the eye.

"When he's about to what?" she asked, giving him a curious little grin.

"Put his life on the line or a least when he thinks he is." Radek pointed to the count down, "I will work on this too, if you would like?"

Elizabeth raised an eyebrow, "You don't think Dr. McKay is right either?"

"No…I believe he is right about Ancients not putting protocol into effect that would cause damage, but I cannot help to wonder why they would build a computer system that could not be used while running system check. Especially when fighting wraith for as long as they were."

She nodded, smiling a little again, "Thanks Radek."

"No problem."

Rodney finished the last few connections to reroute power to the engines in the jumper and crawled out from under the console, pushing his data pad and tools out of the way as he stood and sat in the pilot's chair.

'ON!' he thought, screwing up his face in concentration.

When nothing happened at all he sighed, "Oh come on! I know this works."

"What works?" Carson Beckett's voice called from back end of the open jumper.

McKay's eyes flew open and he turned around, "Carson? What are you doing in the jumper bay?"

"Oh just…having a walk," the doctor nervously came into the puddle jumper and took the seat across from Rodney.

Rodney stared at him for a moment. The man was fidgety, "What is it?"

"Remember when Laura's consciousness was-"

Rodney blushed and turned away from him, "Of course. What about it?"

Carson looked down at his clasped hands, "You kissed me-"

"No!" Rodney shouted then said more quietly, "No…I don't want to talk about that. I thought we were going with pretending it never happened."

"I can't pretend it didn't Rodney," the man whispered.

The scientist turned to Carson and frowned slightly for a moment then his eyes widened, "You mean you-"

"I'm afraid so."

"Well uh…I'm very flattered but-"

"I know you're not into me Rodney, but I needed to tell you to stash it."

"To what?" Rodney really needed him to write down a list of common Scottish sayings.

"To put an end to it!"

"You…don't want me to…like you back?"

Carson gave him a sideways look, "Of course I do…but there's someone else…Colonel Sheppard a-"

The scientist paled, "You and John? He's never said a word to me about…of course he wouldn't because of the Air Force but still I-"

"Rodney I don't-"

Rodney got to his feet and quickly gathered as many tools as he could carry, "Don't worry Carson. I won't say anything about you and John to anyone."

"But Rodney-"

However, before the doctor could say another word the other man had fled the jumper.

"Oh boy…" Carson got to his feet and left the jumper only to find Major Lorne standing just outside the open back.

"Did you tell him?"

"I tried to," he looked at the young man and smiled.

The major blushed and ducked his head. He tried to talk but his voice didn't come out right so coughed to clear his throat, "You tried?"

"Aye, but now he thinks I fancy Colonel Sheppard!"

Lorne choked, "He what!"

"Don't worry. Rodney said he wouldn't say anything to anyone else, but that's not what I'm worried about," he moved in closer to the major who started blushing again.

"What are you worried about?" Lorne whispered, looking into Carson's eyes.

"What Rodney's going to say to John for not being the one to tell him," he chuckled and leaned in to kiss the man before him.

John chewed thoughtfully on his turkey sandwich as he looked out over the ocean from his chair out on the balcony of the mess. He was watching some native gulls flying over one of the piers when the stomach and crotch area of someone blocked his view. Casually he looked up and saw a flustered looking Rodney standing in front of him. He stared at the man innocently and took another bite out of his sandwich and chewed before swallowing, "Do you need something McKay?"

"Uh yes actually I," he wiped his hands on his pants, "Why didn't you-" he stopped and his face twisted slightly as if he were pained.

"Why didn't I what?" John looked down at his sandwich and took another bite.

"Tell me about Carson," he muttered, looking down at the floor.

John's eyes widened, looking around to make sure no one else was in hearing range, "I didn't think I had the right to. I left that up to him. Why does it bother you?"

"No! Uh…no…he just…I wanted you to know that he has or had…a thing for me," he blushed nervously thankful that John was eating out on the balcony and not in the mess like everyone else.

"Oh? He didn't tell me that."

"I figured as much…that's why I wanted to make sure you knew so…you know…"

The colonel eyed him, "Right. Thanks."

"So uh…we're still good right? I mean…even if Carson…" he trailed off looking worried.

"Of course Rodney!" John looked at him confused, "Why wouldn't we be? Just because Carson has a thing for you, you thought I would stop liking you?"

The scientist smiled at him, and John melted. God help him, he was in love with a weird man, "Uh…right…I guess that was kind of stupid…"

"Kinda," John nodded smiling back. He reached over beside him and held out a plate with another turkey sandwich, "I thought you might be along soon so I got an extra."

Rodney blushed and took the sandwich off the plate and started to eat it. 'Why didn't I ask you when I had the chance?' "So I was uh wondering," he took around bite of his sandwich, "I made some modifications to one of the jumpers-"

John's head snapped up, looking at him intently for the first time, "I thought you'd had enough of that?"

"Yes well…that was a rebuilt Jumper. This is a perfectly fine one. I'm running power rerouting scenarios on it to see what lasts longer and what can only be done in desperation."

"And you want me to fly you out to the Main Land and back to see if one you have works?"

"Of course it works the question is for how long and yes…I would. That is, if you're not busy of course."

John thought about the pile of paper work Caldwell had left for him on his desk from his last visit on his desk and to the count down thing going on in the control room. But then he remembered the awful feeling he had when Rodney's jumper had crash landed into the ocean the last time. How he'd almost lost him, "Right now?"

"No actually in the morning. If you're busy then too I could-"

"As long as we're back before the count down's finished, I'll fly you out there. _If_ Elizabeth says it's ok first."

Rodney had a brief vision of everyone standing around waiting for the counter to hit zero. Then when it did, John would turn to Carson and kiss him full on the lips in front of them all.

"Yes…of course. We wouldn't want miss that," he sadly took another bite out of his sandwich.

"Good, I'll just come by your place at what, seven tomorrow morning, if Elizabeth is ok with the test of course."

"Yeah that's-"

"Colonel Sheppard?" Teyla called out from just inside the mess, "I wish to speak to you."

John looked over his shoulder at her, "What about?"

She looked at Rodney, then back at Sheppard, "I would rather speak to you alone, no offense Dr. McKay. It is a…personal matter."

"That's ok," Rodney stood up and waved his half eaten turkey sandwich at them, "we're done."

John watch Rodney's back as he left, but his eyes drifted lower. Teyla moved into his line of vision after a few seconds and stuck him with a look of amusement and annoyance, "So what did you need?"

"It is a custom among my people for the women to choose the man they wish to mate with, however they seek council from their fathers, grandfathers and leader men of the village to help them decide if the man they have chosen is the best one."

John's eyebrows shoot up, "You're asking me?"

"You are the leading man of this expedition are you not? And you are my friend. I trust your judgment and ask your council first."

"Wow," John though briefly he must have a sign on his back that said, 'Come tell me all about your relationships and relationship problems.' "So? Who's the lucky guy?"

She lowered her head and smiled, "I thought perhaps Ronon."

John stared at her a moment, then sighed and smiled. This was going to be a long conversation.


	2. Chapter 2

To all of you who reviewed and liked the first chapter thanks. I need to know when I'm doing a good or bad job on these things even if people don't like to review much, so much thanks to those of you who do. It means a lot.

* * *

It was 6:30 A.M. and Elizabeth was nursing a cup of coffee, while staring at the computer screen in front of her on her desk.

Radek was set up on the other side of the desk marking down things on a sheet of paper, occasionally looking at the tired woman in front of him, "Do you need more coffee?"

"No thanks Radek," she said looking up at him. "I can't believe you stayed up the whole night with me, especially when what we're working on seems to be pointless."

"I don't think that is true. I have been counting up number of articles about the Protocol, we don't know specifics but most are found in the medical part of the database."

She looked up at him, "So you're saying that whatever goes on at the end of the count down as people needing medical attention?"

"No," he pushed his glasses up his nose, "medical check-up."

"Check-ups?"

"And many weeks after. I know very few words in Ancient but," he turned his laptop toward her, "you should look here."

"Elizabeth?" Rodney called from the doorway of her office, "I forgot to ask you yesterday but I need Sheppard to help me run some test scenarios on a jumper. We'll need to take a trip to the main land and back."

She looked up from the laptop, "Are you sure you want to do that Rodney?"

"I'll be fine," he looked at Zelenka, "and someone has to do it, right? I _am_ out in the field the most, so I stand the best chance of needing to actually execute these scenarios at some point."

"Alright," she held his eyes for a while, "just be careful."

"Yes. I do not feel like saving you again," Zelenka never took his eyes off Elizabeth's computer that he was now tapping something out on.

"Ha Ha. Well…I better got back to my room and wait for…the Colonel."

Dr. Weir watched as the man walked off and smiled at his back, "Radek you probably work closest to Rodney of anyone but his team right?"

"Unfortunately for me."

"Well…I know it isn't my place to say it…but I think Dr. McKay has a crush on Colonel Sheppard."

Radek chuckled, "I have noticed and I am not so sure his feelings are not returned. Sheppard is by his side always."

"What about you? Are you sweet on anyone?" she asked, taking a sip of her coffee.

The Czech lowered his eyes, "I would rather not talk about that."

"Why not? Are you in love with John or Rodney?"

"No…they are both…arrogant and I am not attracted to men," he added shaking his head slightly.

"So it's someone you work with?"

He looked up at her for a moment and then gave her a half smile, "Sometimes."

"Does she know?"

"No…probably not…and prefer to keep it like this. Makes working together easier on one."

Elizabeth was silent for a moment and the only sound in the room was the tapping of computer keys, "What if she likes you?"

"I think she is with someone," Radek didn't look up, or sound depressed when he said it, "I am happy for her."

"Oh. You're not going to try to win her?"

He shook his head and looked up at her sadly, "I do not have the right."

Elizabeth blinked at him for a few moments after he had lowered his head then went back to work herself. She would have to finish this conversation with him later.

Rodney was dreading every foot he moved closer to his room. He knew once he got there he would be waiting for the man he loved, who loved someone else. The 'someone else' happens to be a good friend of his…who has or had a crush on him, Rodney McKay.

"Dr. McKay," Teyla stopped him and moved over to stand in front of him. "I am sorry for how I treated you in the mess hall yesterday."

"Its fine," he assured her. "Like I said yesterday, we were done talking and-"

"That is not what I mean," she interrupted him. "Among my people, women choose a man to mate…marry with," she smiled. "We seek the council of our close male friends and family when deciding and Colonel Sheppard was the first I spoke to."

The scientist's eyes widened, "You were asking him if it was ok to marry Ronon?"

Teyla looked at him surprised, "You knew?"

"Well it's been obvious that you…" he trailed off seeing her intent look of calculation at him. "When you came back from that one planet…you didn't seem…as interested in Sheppard any more…and when Ford was holding us hostage you two seemed to…"

She nodded and smiled at him understanding, "You see more than you let on Dr. McKay."

"Well uh…I guess," he looked down at his wrist and realized he didn't have a watch and shook his head, "Sheppard was going to meet me in my room soon. We were going to-"

"I am sorry. I did not realize that you were doing something with Colonel Sheppard today," her look was one of slight amusement.

"Well it was sort of…last minute. Did you…want to talk to me about something or?"

"Yes actually," she looked into his eyes, "I would like_ your_ opinion on my choice of Ronon."

"_Mine_?" Rodney blinked surprised.

"Yes. You are one of my friends as well, Dr. McKay. To not ask you would be an insult and a mistake."

"Well I…I'm not good with the whole relationship…thing and what not but," he looked at her serious, eager face and he sighed, "Ronon seems like…just the person…_guy_ for you. I'm sure you'll be very happy together."

She grinned, "You are not going to give me a talk about respect and loyalty?"

Rodney frowned and shook his head, "No."

"Colonel Sheppard seemed very adamant in making sure I was aware of how I should expect Ronon to act as my…husband?"

"Yes well…that's him. I know you're perfectly able to take care of yourself even against Ronon."

Once again she smiled, but this time she put her hands on his shoulders and bowed her head forward. After a moment of glancing around to make sure no one was watching, Rodney leaned in and touched his forehead to hers.

"Thank you Dr. McKay," she turned and walked off back toward the control room leaving him standing alone in the hall.

A goofy, amused but pleased look covered Rodney's face, "Huh."

John came out of the shower and looked at the clock on his bedside table. It read 6:40, which was more than enough time to get dressed and head over to the mess to pick up a few snacks for the trip to the Main Land.

He had just pulled his pants on when he heard Carson call his name from out in the hall, "Colonel Sheppard?"

"Come on in Doc."

When the Scottish man entered and saw the shirtless Colonel he quickly glanced around, "Am I interrupting something?" he whispered.

"No…I just had a shower. I like to clean up after my morning jog around the city, especially when I'm going to be spending the next few hours in a tight enclosed space with McKay."

Carson gave him a look that asked a question John didn't want to think about right at the moment, "With Rodney?"

"Yeah. He's having me fly a puddle jumper that he's rerouted power in."

"Aye. I saw him yesterday while he was working." He seemed a little disappointed that was _all_ that was going on between them.

John smiled at him, "He came to see me after you talked to him. It seemed he wasn't taking the news very well. Something about me not liking him any more because you had or have a crush on him?"

"Colonel there's something you need to know. Rodney thinks-"

The rest of what Carson said was muffled out by Elizabeth's voice in his ear, "Sheppard this is Weir."

"Hold that thought," John held up his hand for the doctor to be quiet. "Sheppard."

"Dr. McKay just asked me if the two of you could take a jumper to the Main Land."

"He _just_ did?"

"Yes and I've okayed you to go but-"

"We'll be careful."

"Well that's good to hear but that's not what I wanted to tell you," her voice was amused. "I want to make sure that you know to return to the city before the count down expires."

"Why? Have you found something out about it?"

"There are medical records that mention the protocol, but other than that there's nothing so far."

"Medical records?" he looked at Carson who was watching him intently.

"Dr. Zelenka and I are still trying to translate some of them."

"Alright. I'll head over to Rodney's place and pick him up. We'll be back. Sheppard out."

Carson stared at him, "What about medical records?"

John sighed, "Well we haven't made any sort of announcement to the city but, there's a count down that's rolling away up on the main screen in the control room. Rodney just thinks it's the primary system doing a self check for errors, but Weir and Zelenka aren't so sure. They've found this…protocol, as Rodney calls it…documented in medical records."

"Oh my."

"Yeah. She wants us back here before the clock runs out incase there's some kind of emergency. Which means," John glanced at the clock again, which now read 6:55, "that I better go get McKay."

"Colonel, Rodney-"

"Sorry Doc…you can tell me about him later," John left his room picking up his vest and his two guns before heading out of the room.

"This isn't good," Carson mumbled, exiting Sheppard's room.


	3. Chapter 3

"McKay?"

"Coming!" the door to Rodney's room slid open and he stepped out holding his laptop and his vest, "Sorry about that. Teyla-"

"Wanted to talk to you about Ronon? What'd _you _tell her?" John started walking, Rodney beside him.

"I'm alright with it. He seems more her type than-" he paused, and saw John looking pointedly at him, "than anyone else."

John looked forward again grimacing, "I told her to be careful. I mean, he's not the most stable guy in the world."

"Please Colonel, I've seen her fight. She can more than take care of herself and besides I doubt he would seriously hurt her."

"Oh? I guess you haven't seen them spar together then. Even when they're not under some freaky alien drug, things can get violent."

"He follows your orders well enough doesn't he? And Teyla can kick your ass. I _have_ seen that."

"Point taken."

They headed into the gate room, and up the stairs to the control room that was all but empty, except for two techs who were watching the stargate. The countdown was still ticking away and it looked like they had a couple hours before the clock expired.

"Good luck!" Elizabeth called from her office at the two, who were just heading up the stairs.

"You know she's been up all night trying to figure that countdown out?" Rodney shook his head, "The system is simply checking itself for errors."

"She's just trying to make sure before it's too late. If you're right you can 'I told you so' her for months."

Rodney rolled his eyes and walked into the back of the jumper that he had worked on, "Now I had a slight problem with the ignition interface yesterday so…"

John set his stuff down on the floor behind the pilot's chair and then sat down. Unlike most times the jumper didn't flash to life just by him being near it, "McKay? It's not coming on."

"Think 'on' Colonel. The start-up is a bit temperamental, but it's one of the best power conduits I've tried so far."

Sheppard sighed and closed his eyes and then opened them again, "Nothing."

Sighing Rodney got down on the floor and pushed Sheppard's legs aside, crawling under the console on his side.

Looking down on his team scientist like…was leading him down that same path that Carson's look had earlier, "Uh?"

Rodney pushed on his leg, "Move over some more. I can't reach."

"I can't! The chair isn't designed to move that way."

"Well then spread 'em!"

Before John could even move Rodney was maneuvering one of his legs over his chest and under his arm pushing himself forward. He reached up under the panel and moved some connecting wires around, "Anything?"

John flushed hotly as he looked down at McKay looking up from between his legs, "Not ye-"

The jumper came to life humming almost happily.

"Ha!" McKay smiled up at him smugly and then pulled himself back out form under the console.

"It's not going to die on us is it?"

"Only if you turn the jumper off," Rodney snarked at him. "Which while in the _air_ is a stupid thing to do."

John sighed hit the button to open the roof and flew up and out of the city speeding off towards the main land.

After ten minutes of silence, Rodney chanced a glance over at John who was flying the jumper slowly. At least more it was slower than he normally flew.

"So uh…how are things?"

"The jumper is handling fine."

"No I mean…in general."

John gave him a weird look and turned back to looking out the window, "The same as they were yesterday."

"And Carson?" Rodney asked, trying to be nonchalant.

"How do you know I was with Carson?"

Rodney blushed, "I just guessed that you would be since you're-"

"Since I'm what?" John had a feeling that this had something to do with what Carson had been trying to tell him earlier.

"With…him," Rodney was careful not meet John's eyes when he said it.

"Of course I'm with him…I would be stupid not to be. We're close friends."

"Very close friends," the scientist mumbled.

Sheppard frowned, "I thought you didn't have a problem with it?"

"I don't!"

"Well then what the hell _is_ your problem?"

"I need…to…check something…"Rodney got to his feet and went to the back of the jumper and closed the door between the front end and the back.

"Rodney?" John twisted around to look behind him for a moment. "Rodney!"

The other man didn't answer and John frowned and reached up and hit a button then console to try and open the door, but nothing happened. He pushed it again, harder and thought 'open' at the door just in case, but still it didn't shift an inch.

"Rodney, open the door!"

"…"

"Damn it," John mumbled, pushing the engines a little harder so they would get to the main land faster. Soon the jumper was over the beach and the colonel wasted no time in setting down the craft. Rodney could yell at him later about sand in the jumper bay.

"McKay! Open the door!" His fist pounded against the door but the dull thudding echo was his only answer, "You can't keep me trapped in here forever you know."

"…"

Ok. Maybe he could. "McKay. I don't know what's wrong, but I can't help fix it from up-"

The door slid open and Rodney stared back at him. If it weren't for the two damp trails running down his cheeks or his reddened eyes, John wouldn't have thought anything was wrong, more than just a normal McKay outburst of frustration.

"Rodney?" John's voice was quiet.

"I'm fine."

"You're crying. That's not fine in my book."

"Well that's wonderful for you isn't it? _Your book_. What else does this tome of John Sheppard knowledge have to say hmm?"

He opened his mouth to defend himself but Rodney had the quicker tongue.

"I suppose you have all sorts of chapters in it? Like how to seduce people in two smiles or less. Or how to be an arrogant, shallow fly boy. Yes I suppose it has lots of great and insightful knowledge in the _great_ book of John Sheppard."

John was getting angry now, "Now just a-"

"Oh. I 'm sorry. Did I hurt you precious ego? Are you upset that someone's finally seen through all your bullshit!"

"Ego! If anyone has a fucking ego in this ship it's you McKay! And don't even get me started on your _bullshit_. You say you're a genius to anyone with breasts that will listen but half the time you don't have a fucking clue what you're doing!"

As soon as the words had left his mouth, John regretted it. Rodney's eyes were starting to water and his face was screwed up and blotchy, but the rest of his skin was pale and sweaty looking.

He reached out toward the other man silently and touched his forearm. That was all it took for McKay to break down. A garbled sob tore itself free from the scientist and he collapsed forward into Sheppard's chest.

John wrapped his arms around him and held him close, "God I'm sorry Rodney…"

"I d-d-don't know what I'm d-d-doing…" he sobbed, slipping his hands around Sheppard's back, pulling him closer. "I'm s-s-sorry."

"Rodney you _do_ know what you're doing. I didn't mean it."

He felt the scientist pull away and shake his head, "No… I don't."

John pulled him over to one of the benches that ran along the sides of the jumper, "Come on and sit down. You look sick."

"I…I haven't eaten in awhile," Rodney admitted, as he was forced to sit with his legs thrown up over John's lap.

"Well let's see if we can do something about that." Reaching into a vest pocket, John pulled out a power bar. He took it out of the package and held it up to Rodney's mouth, "Come on just relax and eat. Carson would never let me hear the end of it if something were to happen to you."

The man, had been about to take a bite, turned his head way from the food and started to get watery eyes again.

"Rodney?" He took a chance and rubbed one of his hands up the other man's back.

"Don't talk about him…please…," Rodney buried his head into John's neck and sighed, trying not to start crying again.

The colonel's eyes widened. 'That's why he's upset…He's in love with Carson… and he just found out he's dating someone else. Worse yet…Carson told him he had a crush on him at one point too… I wonder if Carson knows…' "Okay we won't talk about him."

They sat in mostly silence, with Rodney's legs over John's thighs. The only noises in the jumper were Rodney's sniffing and the sound of John occasionally rubbing his hand over the man's back.

After a while, John pulled Rodney back from his neck and looked him in the face, "Better?"

"No," Rodney mumbled.

"Anything I can do to make it better?"

McKay gave a bark of a laugh and shook his head, "Nothing that won't hurt Carson."

John frowned and closed his eyes, leaning his head back. 'Why couldn't you have fallen for me McKay?' "Let's go take a walk."

"Walk?"

"Yeah," John opened his eyes and smiled at him. 'Maybe I can't give you Carson, but I can try to give you me instead.'

"I thought Elizabeth said we should get right back?"

"She said we should be back before the count down reaches zero, but she didn't say how much _before_ that she wanted us to be there."

Rodney opened his mouth to say something but John shoved half the power bar into his mouth.

"We've got half and hour to burn. Come on. I want to see if there are any big shells I can give to Elizabeth for her office," he pushed Rodney's legs off of his and stood up, pulling the other man up with him.

"The Athosians haven't found any yet, or she would already-"

"Rodney…don't ruin the moment," he opened up the back of the jumper and watched as the door slowly lowered, "We're going to go hunt for seashells and that's final."


	4. Chapter 4

"Sheppard, this is Weir. Please respond."

John had his arm around Rodney's shoulders, because it was the only touch the man would accept from him a few minutes into their walk, "Sheppard here."

"Are you on you way back to the city?"

"We're working on it," John said casually causing Rodney to give a depressed sigh.

"You're cutting things a little close aren't you?"

"Nah. We needed a break."

Elizabeth heard what John was really saying, 'Rodney needed to take a time out for a few minutes to get refocused.' "Alright. Just get here as soon as you can."

"Will do. Sheppard out."

Rodney turned his head toward Sheppard a little, "Elizabeth?"

"Yeah she wants us to start heading back."

The scientist frowned, "Well it couldn't last forever." He pulled away from John and headed back toward the jumper, leaving the colonel to stand there, looking after him.

"McKay?" he ran up behind the other man, and started walking beside him, "It'll be alright."

He looked over at John and gave him a weak smile, "Yeah…after I get used to this. You didn't need to-" he waved back toward the way they'd just come from.

"I care about you Rodney," John brushed his hand against his as they walked up into the back of the jumper. "Don't let this thing with Carson bother you. I'm sure it won't last."

Rodney stared at John frowning, "You don't want it to last? What kind of person are you Colonel?"

"Rodney, all I'm saying is that it probably won't," he frowned back at him.

"Does Carson know this or is it _insider_ information?" he snapped at him.

"What?"

"The last thing I want to see it Carson hurt, so stop talking and just fly us back to Atlantis," Rodney walked into the jumper and sat in the seat next to the pilot's chair.

John sighed, "Right…"

Elizabeth rested her head in her hands as she stared at the laptop screen. Something about this didn't make since, of course not much of anything had since she joined the stargate program. Her eyes traveled to Radek who had moved out into the control room some time back. She got to her feet without realizing it and before she could stop herself she was standing in front of the console he was hunched over.

He looked up, over the top of his glasses at her, "Did you find something?"

"I…" She kept looking at him and realized he was a serious man, but he had a sweet air to him and it was obvious that he cared about people. Too bad he didn't like children or- "No have you?"

"Only something that worries me."

"What?"

He pointed back to the screen, "I have been looking for way to shut down the protocol if we found out something, but there is no way to. The program was not meant to be shut down after it was started."

"You mean we couldn't abort it even if we wanted to?"

"When McKay said they never had aborted it once it was started, he was correct. However what he didn't look for, was them aborting it before it started. There are times where it was not allowed to start."

"And we weren't aware of the protocol until it did start."

"Yes."

"So there's nothing we can do to stop it?"

"It has already started," Zelenka sighed, tapping something up on his laptop. "That is reason why you cannot shut it down once countdown has come up."

"You mean whatever is happening is actually going on at this very moment?" her voice raised.

"Yes, and it has been happening."

"So we should be feeling the effects."

"If there are even effects to feel," Zelenka sat back and looked at her.

She sighed, "I should make an announcement to the city. Open a channel."

"Alright," he nodded to her when he had.

"Attention everyone, this is Dr. Weir and I have an announcement to make. A protocol in the ancient computer system started running yesterday.

"We are not sure what the protocol is doing, but I have been told, that there's a very good chance that we might already be feeling the effects of whatever it is. If you start to feel any out of sorts, head to the infirmary immediately.

"I would also ask that you please return to your quarters, unless you are headed to the infirmary, until you are told otherwise," she turned and nodded to Radek who shut off the channel.

"Are you sure there's no way to shut it off?" she asked in desperation.

"Sort of removing all power, no, and to stop might be more dangerous than letting it happen."

"And no power means we can't do anything," she turned and walked back toward her office. "I'm going to keep translating. Even if we can't stop this…there has to be something we can do to minimize the damage."

John flew the puddle jumper into the jumper bay and was setting it back down into its space when Rodney, turned to look at him finally. They hadn't said a word to each other the entire ride back, both with their minds deep in thought of how to approach the other.

"I'm going to quiet the team."

"What? Why?" John looked over at him. "You can't."

"I need to."

"No you don't need to. You need to stay on the team."

"I can't stay on the team!"

John glared at him, "Just because Carson-"

"This has nothing to do with him!"

"The hell it doesn't! Every time I mention his name you go pale."

"Because I don't want to think about him!"

"He's one of your best friends Rodney! Pull your head out of your-"

Rodney stood up and walked out the back of the jumper, "I'm quitting the team and there's nothing you can do about it."

"God damn it McKay you can't-"

"Colonel Sheppard! This is Weir!"

"Go ahead," he said stabbing at his head set.

"Are you in the city?"

"Yeah we're headed down into the control room right-"

"Get back in the jumper!"

"What? Why?"

"Now! Make sure Rodney's in there with-"

There was a loud hissing nose and seemed to come from all around John and Rodney, who had been almost to the door paused and watched as a cloud of white gas emptied out of the vent he was standing by.

"What the hell is-"

John's eyes widened, "McKay! Don't breathe any of that!"

"Why n-" an odd look passed over his face and he swallowed came rushing back over to John's side, "Oh god." He whimpered and turned his head away his hands reaching out toward Sheppard only to pull them back against his chest.

The colonel grabbed one of his arms and pulled him into the jumper, closing the back as the white cloud came closer to them, "Rodney? Did you inhale any of that?"

The man nodded screwing his eyes shut.

"What's wrong?"

"Oh god, stop talking…"

"Why? Does your head hurt?" He reached up into the cargo nets and pulled out the med kit. "There should be something in here to-"

"No! Stop!"

"I'm trying to help! Now what's wrong-"

Rodney grabbed his head and kissed him full on with a whimpering moan. Forcibly pulled himself away and grabbed his own head instead, "I'm sorry! I can't…"

John stared at him wide eye panting slightly. He turned his head toward the window at the front of the jumper. The cloud… Without another thought he reached up and grabbed the release for the back end of the jumper and pulled, "Don't be sorry."

"John, no!" Rodney grabbed at his hand, but the damage had already been done.

The colonel inhaled the white cloud that pushed its way inside. He stared at Rodney and swallowed, "Oh…jeez…" His hand that wasn't holding onto the door release reached out and slipped into Rodney's hair and fisted. He pulled the scientist so he was flush against his chest and kissed him hard.

Rodney moaned, trying to pull away and press into the colonel at the same time, which morphed into rubbing against his body wantonly. His hand that had been gripping John's that had wrapped around the release lever, pulled, almost clawing at hand to get it free from the handle.

Sheppard shifted his body slightly and soon he had them flipped around, the scientist pinned against the jumper's wall. He moved his leg in between Rodney's thighs encouraging him to slide against him. He moved his lips from Rodney's mouth down to his neck, his hand fisted in his hair, forcing him to turn his head to allow him access. He released the handle and used his free hand to pin Rodney's above their heads.

"Mine McKay."

Something relational tired for force its way into Rodney's mind and he started to strangle, but was pushed harshly into the wall and bitten sharply on the neck. In surprise more than pain he cried out and went still in submission. A tongue started lapping at his neck and somewhere in the edges of his foggy mind he realized that the colonel had drawn blood.

The colonel growled low in his throat as he lapped up the trickle of blood from the other man's throat. The sound caused a whimper to escape from the wounded man and it fueled the lust that was burning through both of their veins. Reluctantly he pulled away from his neck and pulled on the back of Rodney's head forcing him forward enough to fall to hard his knees.

Rodney reached out up to remove John's pants but his head was yanked back and he gasped out in pain, his eyes watering. The other man got down on his knees, still holding tightly onto Rodney's hair, keeping his head forced back. He reattached himself to the scientist's neck, twisting the both of them around on the grated floor, painfully tearing at the skin on both of their knees. Rodney only fought half-heartedly has he felt John pressing him down onto his back and laying over him, pinning his arms painfully into the textured floor. He felt John reach back behind him for his knife.

Sheppard freed his survival knife, and brought it to Rodney's throat and pressed the point of it into his fleshy skin, just enough to sting. He felt the man stiffen for a moment then relax, accepting whatever was to come next. Carefully, John brought the knife down to Rodney's t-shirt collar and scored the fabric down the center of his chest.

McKay's breathing hitched, when he heard and felt the colonel ripe his shirt open. Then he felt the knife poke into his stomach. His breath quickened and he closed his eyes as he felt John cut into heavy cloth of his pants, just beside the zipper, then down his leg until he reached his ankle.

Tossing the knife aside, John ripped open Rodney's pants. Then his hand moved to Rodney's boxers, which hadn't totally escaped unscathed from the passing blade, and tore those open as well, brushing the cloth aside, uncovering Rodney's cock. John brushed his hand over it grinning evilly at the shiver he felt from the owner.

"Mine."


	5. Chapter 5

John woke up many, many hours later with a head ache and some memories of kinky puddle jumper sex that he wasn't really sure he'd had. There were other foggy memories too. Elizabeth pinning Zelenka to a wall in the control room, Carson spanking Lorne in the mess hall on a table and Ronon and Teyla, wrestling across the gateroom floor…naked.

He sighed and looked around, realizing he was in his own bedroom, lying on a mattress, but not on his bed. Someone, a male someone, was cuddled up next to him with their arm thrown over his waist. They were defiantly awake and defiantly naked.

"Why did you do that?"

John looked down at Rodney's up turned face, "Do what?"

"Open the back? You weren't affected."

"I couldn't let you suffer alone now could I?" he tried. But he could tell Rodney wasn't buying it. "I wanted you to forget about Carson…and like _me_ instead…"

"What!"

"It didn't work like I wanted it to but-"

"Wait… _me_ forget about Carson? You're the one that's dating him! How could you cheat on him just help me forget about him?"

"I'm not dating Carson! Who told you that!"

"Carson did!"

"He's dating Lorne! He told me about it and I said I didn't care and wouldn't say anything to anyone. I told them would back them up if anyone did find out."

Rodney stared at him, "So you…_aren't_ dating Carson? You're _not_ in love with him?"

"No!"

"Oh…uh well…" Rodney blushed.

"You're the one that's in love with him! He told you he was with someone, which you thought was me, after he told you he had a crush on you. You liked him and were upset. That's why you've been so pissy lately," he reached over and caressed Rodney's cheek, looking at his frowning lips. "Now I know I'm not Carson-"

"John I don't-"

"–and I know you don't like me…well not as much as I like _you_ obviously but-"

"No," Rodney said loudly, interrupting him. He made sure he had the other man's attention before he spoke again, "I don't like _Carson_."

"What do you _mean_ you don't like Carson? You were upset wh-" John stopped mid-word and looked down at Rodney who was blushing even more, but looking at him intently, "_Me_?"

"Well yeah. I mean doing get me wrong the accent is hot but," he lifted his hand and waved up toward John's head, "that's nothing compared to rakish hair…and the neck obsession thing."

John gave a sharp laugh and closed his eyes, leaning his head against Rodney's, "God I'm such an idiot."

"Yes well," Rodney patted his shoulder, "you're forgiven."

John opened his eyes and leaned up, kissing Rodney's forehead, brushing back his hair, feeling it in between his fingers. He swallowed sharply. A memory of pulling back Rodney's head back painfully far floated into the view of his mind's eye.

"I'm sorry that I hurt you," he whispered, frowning slowly down at the other man.

"I…" Rodney coughed a little and look up at him from under his lashes, "I didn't mind."

"I'm still sorry," he placed a few small kisses on his forehead before he pulled back. "We should go see how everyone else is."

Rodney nodded but then groaned.

"What's wrong?"

"Elizabeth is going to _kill_ me!"

John and Rodney quickly dressed and left the colonel's room in search of other people waking up from the drug induced coupling.

The first people they found was actually the best ones they could have. Carson was walking around with Lorne at his side, medical bag in hand.

"I see you two made it through this," Carson gave John a look. "No everyone was as lucky to be around someone they were in love with. Elizabeth made an announcement but-"

Rodney realized what Carson had actually said to John, "You mean you _knew_?"

"Son, I bloody well told the man about Keith! Do you think I'm so dense as to tell someone that I didn't know I could trust?" Caron turned his attention back on John, "I trust the two of you figured things out then?"

"Yeah…I even figured out what you wanted to tell me about him," John nodded to McKay who frowned.

"I can't believe you let me leave, thinking you were with John!" Rodney looked at Lorne who didn't look happy about that either.

"There wasn't a lot I could do Rodney! You bloody ran off!"

"Ok! Let's not get into a fight over this," John stepped in between the two men. "Have you found Dr. Weir yet?"

"No. Not yet. Have you checked her room?" Carson asked them pleasantly.

"We haven't checked any where yet," Rodney stated, still looking ticked off.

"Well she was with Dr. Zelenka, so she should be there," Carson smiled at the both of them before walking off toward the mess hall.

"Why do you say that?" Rodney looked at him as if he knew something and he wasn't telling them.

"Elizabeth is the more dominant of the two."

"What does that have to do with anything?" Rodney snapped.

Lorne walked past them and gave them a cocky grin, "Where did the two of _you_ wake up?"

John glanced at Rodney who was blushing, "We get it. Thanks Major."

"No problem Colonel."

"So? To Elizabeth's room?"

"Right."

Dr. Weir opened her eyes and sighed, deeply. The sun was pouring in her bedroom window which meant it was late in the afternoon.

"You're awake."

She sat up, pulling the sheet around her chest, "Dr. Zelenka! What are you-" and then a memory of him pinned against the wall at her mercy, making him beg her for release, denying him any for hours, until she finally thought he deserved it, came to her. She blushed, looking at him apologetically.

Radek was sitting in a chair across from her bed, wearing only a pair of grey sweat pants. His glasses were off, his hair was messier than usual, and he looked a lot like he did after the siege on the city, their first year in the Pegasus galaxy, "Did you figure out what the protocol was about?"

Elizabeth dropped her head, "The Ancients wanted to make sure that they would never get so busy that they would forget to have children. They saw the problem the Asgard would have, long before they did and wanted to make sure _they_ never had to deal with it. The medical records were pregnancy follow-ups. That's also why they used it as a passage of time…" She looked at him, "If I'm-"

"We will get married."

"Radek…You don't even like children," she smiled slightly, moving her hand over her abdomen. "I wouldn't ask you to help me or to marry me, even if you did. I can't ask you to give up your work for me."

"I _want_ to marry you," he looked over at her, "even if you are not carrying my child."

Her eyes went wide in surprise. She didn't know what to say.

"Dr. Weir?"

"Elizabeth?"

He smiled at her before he called out to John and Rodney, "In here."

"Radek?" McKay looked away from him to Elizabeth who was obviously naked under the sheets. "You don't like kids."

"I know," he sighed leaning back in the chair, closing his eyes, scrubbing over his face with his hand.

"Huh…anyway Elizabeth-," Rodney focused back on the matter at hand as John came up behind him and stood.

"Rodney she's naked!" John's hand went to his waist and he tried to pull the scientist out of the room.

"She's not naked. She has a sheet on!"

"That isn't the point! At least let her get dressed first before she has to yell at you."

She watched the two of them, her eyes going right to John's hand that was still at Rodney's waist, "I'm not going to yell at him-"

"Ha!"

"But when I'm giving birth…when _all_ of us are…_you're_ going to be in the room."

** Epilogue **

"Emily, be careful!" Elizabeth called out as her seven year old daughter ran past her, out of the lab, carrying something that looked like it might be a mini naquadah generator.

"Oh Elizabeth just the person I wanted to see!" Rodney moved her over to where his team was working on combining a wraith damaged wraith dart with a damaged puddle jumper, "The puddle dart should be ready in a few more days. The dart system is growing nicely into the interface."

"Good. Where's Radek at?"

"He's inside working on the DHD," Rodney pointed through the window of the jumper.

She smiled, "Is that why Emily was allowed out of here with a mini naquadah generator?"

McKay's shoulder stiffened, "As her godfather I thought she should be allowed to expand her mind into the vast reaches of the science world. Radek's been holding her back with just parts and no power source."

"She's seven Rodney…" she smiled at him. She had happily made Rodney and John Godfathers of Emily. Mostly so she could guilt trip them into watching her sometimes, but now the two men were just as much her parents as she and Radek. "And he was doing that because I told him to."

"Yes well it's not like I'm teaching her how to fly puddle jumpers or anything! That generator can hardly power her room."

"All the same-" Elizabeth sighed. She knew she wasn't going to win this fight. Rodney thought of her as his genius daughter.

"Shep! Put me down!" Emily giggled, as John carried her in and set her down in front of Rodney and Elizabeth. She was still holding onto her little generator but now she had some another device in her hand.

"Is that a personal shield?" Rodney pointed to the green thing in her hand.

"I saw her messing around with it, so I decided to let Rody tell her why personal shields aren't toys," John rubbed her head of short dark hair, messing it up.

"I was recharging it!" she grinned at Rodney who frowned down at her angrily.

"This is a very dangerous piece of Ancient technology!" Rodney pulled it out of her hand, "You could get stuck inside the shield!"

"It wasn't for me!" she glared at him.

Elizabeth looked down at her, "Who was it for?"

"Kayon," she held out the naquadah generator to Rodney who took it gently from her hand. "He's always getting beat up by the other boys."

"Honey…Kayon doesn't have the gene," Dr. Weir brushed back her hair from her forehead.

Emily pouted, "Ronon said that he had to learn to fight for himself and Teyla said the same thing. I wanted to make it so he didn't have to fight."

Radek came out of the back of the puddle dart and came over to see what was going on, "Is that a personal shield? That brings back memories."

"Your _daughter_," Rodney said turning toward him frowning, "was trying to recharge it so she could give it to Kayon to wear."

"Why is it when she does something wrong you say she is my daughter…but when she does something amazing you say she is your goddaughter?" Radek looked over the top of his glasses at him "Did she do it?"

"Radek!" Elizabeth scolded.

"Not yet," Rodney looked into the back of the device, "but I think she's onto something."

"Rodney!"

He looked up at Elizabeth, "What? She is!"

"Rody?"

"Hmm?" Rodney looked down at Emily, trying to ignore Elizabeth's glare.

"Is there a way to turn the personal shield into a personal cloak? Like you told me you did with the city?"

The room went silent and Rodney and Radek stared at her in shock.

"Why didn't we think of that?" Rodney asked looking down at her amazed.

"I don't know…" Radek blinked staring off into space, "It is a very good idea."

"Emily do you want to help-" Rodney started to ask.

"I will not have _my_ daughter messing around with a personal shield and cloaking technology when she's seven years old," Elizabeth frowned at her husband, who sighed.

"We could always teach _my_ goddaughter how to fly a puddle jumper like a fighter pilot," John smirked down at Emily who grinned back.

Everyone turned toward him and started to protest and John shrugged, smiling at the giggling Emily, "Worth a shot."


End file.
